Two reproductive isolated morphs of Arctic charr (Salvelinus alpinus), termed profundal and littoral charr according to their different spawning habitats, co-occur in the postglacial lake Fjellfrøsvatn in North Norway. All profundal charr live in deep water their entire life and have a maximum size of 14 cm, while the littoral charr grow to 40 cm. Some small and young littoral charr move to the profundal zone in an ontogenetic habitat shift in the ice-free season and the rest of the population remains in epilimnic waters. The two morphs had different diet niches in the profundal zone: the profundal charr ate typical soft-bottom prey (chironomid larvae, pea mussels and benthic copepods), while the young littoral charr mainly consumed crustacean zooplankton. In four other lakes without a profundal morph (i.e. monomorphic populations), young charr also performed ontogenetic habitat shifts to the profundal zone and fed on zooplankton. The profundal morph of Fjellfrøsvatn therefore utilize a food resource niche that neither the littoral morph nor comparable monomorphic populations exploit. This suggests that intraspecific resource competition has driven incipient ecological speciation of the profundal charr of Fjellfrøsvatn. The exploitation of the soft-bottom resources by the profundal charr supports earlier experimental findings that the profundal morph is genetically different in trophic behaviour and morphology. The sympatric ecological divergence within the profundal habitat is possible because unexploited food resources (soft-bottom profundal prey) are available. Apparently, this represents a case of incipient segregation by expansion to new resource types (niche invasion), and not by subdivision of one broad ancestral niche.